Ontology-based Interactive Information Extraction from Scientific Abstracts

Milward D, Bjäreland M, Hayes W, Maxwell M, Oberg L, Tilford N, Thomas J, Hale R, Knight S, Barnes J.

BioLINK SIG Text Mining Workshop, ISMB/ECCB 2004




Over recent years, there has been a growing interest in extracting information automatically or semi-automatically from the scientific literature. This paper describes a novel Ontology-based Interactive Information Extraction (OBIIE) framework and a specific OBIIE system.

We describe how this system enables life scientists to make ad hoc queries similar to using a standard search engine, but where the results are obtained in a database format similar to a preprogrammed information extraction engine. We present a case study where the system was evaluated for extracting cofactors from EMBASE and MEDLINE.